.. _topics-index:

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Welcome to GreedyFHist's documentation.
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.. toctree::
  :caption: Menu
  :hidden:

  installation


.. toctree::
  :caption: usage
  :hidden:
  
  pairwise
  groupwise
  config

.. toctree::
  :caption: API
  :hidden:

  api

.. toctree::
  :caption: LICENSE
  :hidden:

  license

GreedyFHist is a Python based tool for registration of stained images.

For examples in using GreedyFHist's commandline interface, see ``examples``.

For examples for interactive Python sessions, see the provided examples: ``examples/notebooks/groupwise.ipynb`` and ``examples/notebooks/pairwise.ipynb``

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Citing
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.. note::

    @article{wess2024spatial,
      title={Spatial Integration of Multi-Omics Data using the novel Multi-Omics Imaging Integration Toolset},
      author={Wess, Maximilian and Andersen, Maria K and Midtbust, Elise and Guillem, Juan Carlos Cabellos and Viset, Trond and St{\o}rkersen, {\O}ystein and Krossa, Sebastian and Rye, Morten Beck and Tessem, May-Britt},
      journal={bioRxiv},
      pages={2024--06},
      year={2024},
      publisher={Cold Spring Harbor Laboratory}
    }